Plug flow separation water management systems are known to provide for settling of grit and heavy particulate and to float oil and floatable particulate by providing one or more plug flow conduits between adjacent settling chambers within an in-line flow container. A prior STORMGATE SEPARATOR™ system used a circularly cross-sectioned transfer opening between an inlet chamber and a first settling chamber, that caused undesirable turbulence and poor plug flow control of water through the system. That system also featured a rectangular flow duct frame between the first and a second settling chamber. Flow of water through a second circular transfer opening between the second settling chamber and an outlet chamber was controlled by a rectangular baffle or orifice box covering the opening. The stormwater bypass weir elevation was field-adjustable. In the prior art STORMGATE SEPARATOR™ system the inlet pipe was aligned with the long axis of the first settling chamber but the outlet pipe was transverse to the long axis of the second settling chamber. In other words, the inlet and outlet pipes with the overflow weir therebetween were at right angles to one another rather than being aligned or in-line with excess stormwater bypass flow.